Burrowing owls (Athene cunicularia) on the Pawnee National Grassland in Colorado nest on black-tailed prairie dog (Cynomys ludovicianus) towns where periodic extinctions from plague (Yersinia pestis) have been studied since 1981. Plague, a non-native pathogen, is typically lethal for prairie dogs and leads to loss of owl nest sites and other habitat changes that may affect owl productivity. Our goals were to 1) apply a new mark-resight model to estimation of owl productivity and juvenile survival, 2) examine the relationship of owl prey use with plague, precipitation, nest density, nest success, and fledging success, and 3) determine how nest abundance, nest success and fledging success were influenced by plague and rainfall. We monitored 310 owl pairs and collected diet samples from 2005 – 2008 on extinct, recolonized, and active prairie dog towns. Nine sampled prairie dog towns were extirpated by plague during this study, and each was recolonized by prairie dogs within the year. In 2007 (a poor year for owls), survival from emergence to fledging (50%) was higher for heavier owlets in better condition. Productivity was underestimated, but improvements to the mark-resight protocol should yield unbiased estimates in the future. Owls in dry years and those at successful and very productive nests ate fewer birds and more mammals. Plague was largely unrelated to owl diet, suggesting that the effects of plague on owl populations result from changes in prairie dog presence, burrow availability, or landscape heterogeneity rather than prey populations. Nests occurred at higher than average density and were mainly successful on recently recolonized towns.